One Final Mission
by Mandalorian Runescaper
Summary: Commander Shepard awakens after months in hospital to be told that the Reapers are gone. Just because the greatest threat the galaxy has ever faced has been defeated, however, does not mean his battles are over. There is one last quest to undertake, but it could cost him the thing he holds most dear. Feedback is much appreciated!


**A/N: Okay, so this is my first attempt at a pure Mass Effect story. Please review and let me know what you think if you can spare the time. Be honest as well. I love praise as much as anybody, but constructive criticism is also much appreciated.**

**My favourite ME stories written by fellow fans have almost always been the ones that don't just rehash the games. Don't get me wrong, there are some excellent stories out there that follow the first three instalments closely, but even so, I've often found the best ones (again in my opinion) were those that took an aspect of the universe we know little about and expanded on or twisted something about it. The First Contact War is a great example of this, so this is my attempt to do something similar.**

**I'll probably turn this into a full story once I finish my current main one if there's enough interest. Anyway, that's enough from me. I hope you enjoy!**

**Chapter 1: Acceptance**

The entire shuttle shook violently as it began to enter the atmosphere, the force enough to cause Shepard to stagger slightly. He winced at the stab of pain that erupted in his left thigh in response to the powerful vibrations that could be felt within the cramped confines of the Kodiak, the sensation a reminder that he still hadn't fully recovered. Perhaps he never would.

The fact he was still alive was a miracle. No, when he had cheated death for the first time, that had been a miracle. How he was alive now, after having sustained wounds that would have killed any other human… well, he honestly couldn't think of a word to describe it.

When he had awoken in a hospital bed on Earth to be told he was slowly recovering from his wounds he had laughed. There was no way that was possible, he had told the doctor who had been standing at the foot of his bed. Cerberus bringing him back the first time after he had been, for all intents and purposes, dead? That had been a stretch. More than a stretch, given how long it had taken him to even accept that he was still him, not a clone or something similar.

Yet here he was standing in full N7 armour, surrounded by Alliance marines, waiting to land on the planet below and disembark. It could have been just another one of the dozens of different missions he had taken part in before the beacon. Before taking command of the Normandy. Before—

Shepard cut that line of thought off before it could arrive at its conclusion. He had still been in a hospital bed, albeit a different one after being relocated to an Alliance cruiser, when he had heard the news. He hadn't believed it. No, he had refused to believe it. Not because it seemed as impossible as him still being alive did, no what he had learned was happening certainly was plausible. But what it could represent was terrifying. Everything he had fought for, everything he had achieved…

The Kodiak shook again, though it was less violent this time. That was unsurprising; they were in the planet's atmosphere now. The occasional bouts of turbulence they could expect during their descent through it would be nothing compared with the initial one. The soldiers around him ignored it, so he did too, even if his thigh made it more difficult than he would have liked. His mind turned back to what he had been told just after being moved to the cruiser. The Reapers had been destroyed. The geth had met the same fate, but even that paled in comparison to what had been revealed next. The knowledge that there was a very real possibility—

"All right, ladies."

Captain Andrews' words caused everyone to turn and face him, though the two female squad members were the only ones bar Shepard not to make a good-natured sound of protest. "We handle this just like we planned," the tall Englishman continued. "We land, find the insurgent, and take him alive. Assuming he's even real." He turned to face Shepard, who stood up straighter, years of training kicking in despite how his mind continued to race.

"Remember, Commander, you're only here as an advisor. If I had my way, you wouldn't be here at all. Stay by the shuttle with the man I leave to guard it. No heroics."

Shepard nodded while muttering a quiet affirmative. Hackett had nearly court-martialled him in an attempt to prevent him from taking part in the mission. The admiral had gone through every reason he could think off to try and persuade him not to go, all of them valid and sensible. He hadn't fully recovered. He had done enough and had the right to retire from active service. He was too close to one of the parties involved.

That last one was the biggest concern the senior officer had voiced.

Hackett was a good man, though, and he had obviously picked up on the fact Shepard wouldn't budge. Reluctantly, he had given the go ahead for the N7 to participate in the operation in an "advisory capacity." The quotation marks had been obvious when he had relented. Shepard was under no circumstances to participate in combat or even stray much beyond the shuttle, and he certainly wasn't in command. It was Hackett's way of letting him go without allowing him to really do anything.

Normally the knowledge that others might put their lives on the line while he effectively sat back and did nothing would have chaffed. Shepard had always believed in leading from the front, an approach he had adopted from Anderson early in his military career. Saren and the geth, the Collectors, Cerberus, and finally the Reapers. Against each of them, he had fought side by side with those he commanded, his friends—and they were friends, not soldiers—giving every bit as much of himself for them as they did for him. Had the shuttle been heading towards any of those enemies he had fought before, he would have refused Hackett's offer and insisted that he fight alongside those serving with him, regardless of the fact he didn't know them.

But they were not heading for any of his previous enemies.

The voice of the pilot suddenly filled the main body of the shuttle, his voice distorted only slightly by static. "ETA one minute. Still no sign of activity, but watch yourselves down there. Just because we haven't seen much of anything doesn't mean there's nothing."

"Roger," Andrews' response was clipped and to the point, very professional. "Final weapons check, boys, then brace." His gaze returned to Shepard.

"Stay with the shuttle. No heroics."

"That's right." The sound of thermal clips being removed, examined, and slid back into their respective weapons filled the cramped space for a moment before quieting. Andrews remained silent throughout, only speaking again when the last weapon had been checked. "We've got this, Commander," he said, speaking more softly now. "You just watch yourself down there."

Shepard nodded distantly, waiting for the shuttle to touch down.

* * *

It was more… normal than he had expected.

As Shepard exited the shuttle, only after the marines had first secured the area, the first things he saw were the buildings. All of them were of the same blocky style common to many Alliance colony worlds, the design have been optimised for both easy storage inside the ships that brought them to where they were needed as well as durability. Each building was coloured the same uniform grey, the only variety present being the occasional splash of dull orange, which took the form of stripes on the sides of some of them. In short, the dwellings were drab, functionality taking far greater priority than appearance. There were no signs of life, but that was to be expected. He had learned during the journey that the colony was one of the many that had been evacuated during the early days of the war with the Reapers. There hadn't been time for him to be briefed; Hackett had added him to the mission at almost the last minute.

A thin layer of sand covered everything, including the landing pad on which he stood. It was almost as unappealingly coloured as the structures it clung to, being such a dull shade of brown it looked almost grey. A sudden gust of wind caused a cloud of it to strike Shepard's visor, the impact of the grains inaudible, though they still impaired his vision. As the wind grew stronger, he was forced to rub the front of his helmet in order to remove the offending matter so he could see properly. Ladon, as he remembered the world had been called by one of the marines, certainly didn't make a good first impression.

"Commander."

Shepard turned his attention to Andrews, who gave him a nod before inclining his head towards the heart of the colony. "The boys and I are going to head further in before whoever might be here has time to set up too many surprises. I'm leaving one of them behind to guard the shuttle like I said earlier. Make sure he doesn't do anything stupid."

Wordlessly, he nodded in reply, eyes following the squad as they departed, leaving boot marks in the sand as they went, all but one of the members taking the single set of stairs that led down from the landing pad and into the colony proper. Ignoring the marine who marched over to the shuttle and stood with his back facing it, he resumed his examination of his surroundings.

Even though nothing looked out of place, Shepard felt uncomfortable. Not just because of the very real possibility that what they were looking for was indeed present in the colony, but also because his surroundings brought back too many memories. He had seen plenty of colonies just like this one. Horizon during his time working with Cerberus against the Collectors. Countless others during the war against the Reapers, trying desperately to save as many people as possible in between efforts to unite the different races of the galaxy…

And Freedom's Progress.

Even though there was nothing wrong with his armour's air supply, Shepard's hands rose to his helmet almost of their own free will, scrabbling at the release before finding it and allowing him to pull it off. Gasping heavily but still finding it difficult to breathe, he lurched forwards, staggering a few steps away from the shuttle before collapsing to his knees. Even though his eyes stared directly into the metal plating of the landing pad upon which the vessel behind him rested, he saw something that could not have been more different as he knelt there.

Staring back at him were a pair of glowing white eyes, tinted slightly purple as a result of the nearly opaque piece of glass-like material that covered them. Shepard blinked and suddenly they were gone, only a section of landing pad staring back at him now. Trembling slightly, sweat breaking out across his forehead as he fought to control his breathing, he almost didn't hear the marine who had been left behind as he spoke.

"Sir, are you all right?" The owner's tone carried genuine concern at his state. "Do you need me to contact the squad medic?"

Shepard grunted, struggling to his feet with difficulty before turning to face him, noticing with relief that the wind had stopped for the moment. "That won't be necessary," he managed. "If they encounter anything out there then they might need him. I'm fine, soldier, just a bit overwhelmed to be back in the field."

It didn't feel right lying to the man, but what was the alternative? Tell the truth? Hackett had already informed him, in the strictest confidence, that while he had no doubts about Shepard's loyalty, his view wasn't shared by everyone within the Alliance hierarchy. If not for the current situation, that people still questioned his repeated decisions to fill his crew with both humans and non-humans would have been infuriating. But given what he had been told already…

"Are you sure, sir?"

"I'm sure," Shepard muttered, waving the man away as he made to approach, drawing an unconvinced nod from the marine as he remained standing by the shuttle. To be honest, Shepard felt pretty sorry for him. While the other man was covered from head to toe in the trademark dark blue armour worn by Alliance marines, Shepard could tell from his voice that he was young. He definitely hadn't served on the front lines against the Reapers, given how his armour lacked the dents and pockmarks some of his squad mates had decorating theirs. Were he still that sort of age, all he would have wanted, had he been in the other man's position, would to have been allowed to go out there with the others into the thick of the action, not be stuck minding a last minute addition as well as the ship.

"Guard duty," as it had been accurately but also derisively called by marines long before Shepard's time, was a mostly extraneous duty in an age where an orbiting ship could normally detect a threat long before the human eye could. On top of that, standard Alliance procedure held that all routes to the evacuation vehicle be supervised at all times, meaning it was incredibly rare any hostiles approaching it wouldn't be found and neutralised before they had line of sight on the vessel. Even so, it was better to be safe than sorry, even if the kid was probably bored out of his mind

Turning his attention back to the colony, Shepard winced as he tried to avoid concentrating on any of the countless memories that clamoured for his attention. Most he was able to dismiss easily, but by far the hardest to ignore was the one he had seen when he had fallen to his knees.

Those glowing eyes.

Where was she now? Was she safe? Had she been as horrified as he had when she had learned what was happening and what could occur as a result? Was what had occurred already why she hadn't been there when he had awoken? That had been the first sign something was seriously wrong. The doctor had told him he had been out for months, but he knew Tali better than he knew himself. She would never have allowed herself to be far from his bedside, just as he would never have allowed himself to be far from hers if their roles had been reversed.

His thoughts were interrupted when he noticed the marine was occasionally glancing over at him as he remained standing in place, the man trying and failing to be inconspicuous while doing so. Scowling when he found himself unable to ignore the looks being constantly thrown his way, Shepard folded his arms across his chest and stared directly into the other man's eyes, causing the marine to flinch slightly at the intensity of his gaze.

"What?" he asked flatly.

"I… I'm sorry, sir," the soldier opposite him apologised, words tumbling out over one another. "I just, um, wanted to ask you something."

Feeling his temper cool as he realised the marine was not about to ask whether he was okay for a second time, Shepard nodded once. "Go ahead," he replied, voice a little less confrontational than before.

"I… wanted to ask for… for advice," the soldier managed, voice quiet as he did so. "There's a, um… that is to say… some of the guys said you had an asari girlfriend once, and I had a fight with mine. How do I, ah, make it up to her?"

Shepard stared at him motionlessly for a few seconds, causing the marine to shift in discomfort. Seeing that, he couldn't help it. He laughed.

"Sorry," he forced out in between noises of amusement, easily able to pick up on the other man's irritation at his response. "I'm afraid the rest of the squad have probably been spending too much time on the Extranet. I've never been in a relationship with an asari."

"But Doctor T'soni—"

"Is a very good friend."

"I… right," the marine nodded slowly, but in a way that made it clear he believed what he was being told. "You still served with her when you went after Saren and then with the Reapers, right? You must have some pointers."

"Not many, if I'm honest. Asari may not technically be women, but they are definitely similar in a lot of ways." Shepard paused for a moment. "How would you apologise to her if she were human?"

"I don't know." The marine was shuffling his feet in a way that was decidedly unmilitary now. "I wouldn't have said what I did if she weren't an asari."

"So what did you say?"

The soldier looked away before seemingly noticing the movement of his feet, since they stopped moving. "I, um, was meeting her parents for the first time," he muttered so quietly Shepard had to lean closer to hear him. "They're both asari, even though I know her people have a thing about that. I may have… thought aloud that… ah… they were hotter than her."

If Shepard had laughed before, it was nothing compared with now. His eyes watered as he fell back to his knees much more heavily than the first time that day, the flare of pain that shot up his bad leg nothing compared with the all-consuming need to laugh. And it was a need, he suddenly realised. Knowing what he did, he needed to take his mind off it, just for a moment. The marine, suddenly looking as though he had shrunk several inches, only caused him to laugh harder, both hands on the floor of the landing pad to steady himself.

Eventually, Shepard managed to get control of himself, struggling back to his feet with difficulty, shoulders trembling with the aftermath of his mirth. Wiping his eyes with the back of his hand, he waited until his voice was at least understandable before replying. "Have you…" he nearly started laughing again, "tried saying you didn't mean it?"

That the marine's voice was coloured with anger only made it harder for Shepard not to lose it again. "Of course," he snapped. "Over and over again. I had to return to duty last week, but she won't answer me whenever I message her." His voice turned sad towards the end, which brought Shepard back down to earth a little bit. "What do I do, sir? I think I… I think I love her."

"Look, kid," he replied, walking over and clapping a hand onto the other man's shoulder, much to the latter's surprise, "if it's only been a week then you can afford it give it a bit longer. Asari live much longer than humans, so she probably just needs a bit more time to process what happened. Do you think she feels the same way about you?"

"I… I think so."

"Good," Shepard smiled gently, patting the shoulder he held before releasing it. "She'll probably give you a bit of grief for what you said, but you'll just have to tough it out. If she feels the same way about you, she'll come round. She probably thinks she's overreacted by not talking to you at all for the last few days and is a bit embarrassed about it."

"I… Thank you, commander." The gratitude in the man's voice made it clear he meant it, which only caused Shepard's smile to widen.

"No problem, kid."

"Can I ask you something else?" Shepard felt his heart sink a little at the enthusiasm in the other man's voice. He had heard that tone many times before, often after speaking to someone who had been rather shy at first but then decided they would try to convince him they were his biggest fan. That was not to say they were, Shepard had actually met his biggest fan. On multiple occasions, unfortunately, the experience not being one he was keen to repeat again. Even so, he remembered his earlier thoughts.

The kid was probably trying to stave off boredom. If he were honest, so was he. They might have only been on the ground for a few minutes, but despite his injury Shepard was beginning to feel as though he should be more involved in the operation. It wasn't even the result of following orders rather than giving them, it just felt wrong that others should be risking their lives while he was comparatively very safe. He might have accepted the situation earlier when they were still in the air, but his opinion of it was starting to sour.

Glancing around at his surroundings just in case anything had changed and finding nothing out of place, he nodded once to the other man, who didn't seem to notice his hesitation as he eagerly began to speak. Only a few seconds later, however, Shepard frowned, the marine's voice turning into a series of incomprehensible noises as he noticed a brief flash of yellow next to a building about one-hundred metres from their position. It was so quick he could have very easily imagined it, especially considering he was not completely fit. As his companion began to ask if he'd heard his question, Shepard positioned one hand so it faced the ground, palm flat as he waved it several times; the almost universally recognised command to get down.

Dropping down onto his front, he was suddenly very glad of the shape of the landing pad. While it sat no higher than the buildings that surrounded it, being only a couple of stories off the ground, its edges curved upwards slightly, giving it an almost bowl-like structure, though it was extremely shallow. As Shepard rolled over to the far right of it, he noted with relief that the side he was now pressed against was tall enough to shield him from the view of anyone in that direction, provided they did not stand virtually on top of him.

"Sir?" The unnamed marine had begun to take cover on the opposite side to Shepard. "Did you see something?"

"I don't know." Shepard felt more than a small amount of frustration. It could easily have been nothing. After all, what kind of insurgent would wear a bright colour like yellow instead of a darker colour that would be less likely to attract the eye? Even so, his instincts told him they were not alone. "I think I saw something. Get over here, but move slowly."

Wordlessly, the other man nodded and began to crawl over to him while lying flat on the ground, using his elbows rather than his hands in order to reduce his profile. Slowly drawing the Carnifex he had attached to the small of his back before getting on the shuttle and gently clicking the safety off, Shepard took a deep breath, allowing himself to slip into a very familiar mind-set. There were no buildings taller than the landing pad, meaning if they had been seen by someone they couldn't be fired at from afar if they kept their heads down. There was also only the one way up to their location, meaning that was where an attacker would have to approach from.

The Kodiak sat in the middle of the landing pad. Shepard was currently positioned more towards the opposite end relative to the stairs that led up to it, meaning the ship obstructed his view of them. His companion was as far back as Shepard but had almost reached him by this point, crawling past the rear of the ship to close the distance between them. Inching forwards while still hugging the wall to his right, Shepard slowly made his way round the Kodiak, the top of the stairs gradually coming into view. Levelling his weapon in their direction, he softly called out to the man behind him.

"I have a visual on the stairs. They're the only way up, so if anyone's coming we have the drop on them. Contact Andrews and tell him we might have seen something."

He barely heard the marine's quiet affirmation as he began to contact the man in charge of the mission. Shepard's eyes remained locked on the top of the stairs, the hairs on the back of his neck standing on end. There was something he was missing, he realised with a sinking feeling of dread. Something he would have noticed already if he hadn't just spent several months unconscious in a hospital bed. Unbidden, his eyes swept over the boot marks the marines had left when they had departed towards the stairs.

Which was when he noticed there was a pair of foot prints heading in the opposite direction.

His gaze followed the tracks, which were certainly not human. They led round the ship in the opposite direction to where he and his companion were lying prone, vanishing behind the bulk of the Kodiak. Swallowing heavily, Shepard quickly rolled over onto his back, raising his Carnifex and staring down its sights at the figure that was crouched just behind the rear of the shuttle, using it as cover as they aimed their own pistol in his direction.

They fired first.

The sound of kinetic barriers shattering filled the air just before he fired back, the first shot from his weapon knocking out the attacker's own shields, the sheer power of the Carnifex more than a match for them. His second caught the newcomer right where their heart was, a gurgling noise escaping their mouth as they fell backwards and crashed to the ground, dead before they even hit the floor.

Staggering to his feet and keeping his weapon trained on his attacker, it was only then Shepard noticed his shields were still active. His mind raced at the observation. He had definitely heard more than one set go down. But if he hadn't been hit…

His head snapped round, eyes widening at the sight of the figure still lying on their front by the wall at the edge of landing pad. A rapidly growing pool of blood surrounded the marine, tiny grains of sand vanishing beneath the sticky red liquid. Shepard lurched forwards, omni-tool activating as he prepared to give him a dose of medi-gel, only to stop as he saw the small hole between the man's helmet and the armour that protected his back. The shot had punched right through one of the weakest parts of his protective shell and entered his neck.

_Damn it, kid. I'm so sorry._

The tendons in his hand feeling as though they might snap as his grip tightened on the pistol he still held, Shepard marched over to the corpse of the marine's killer. At a distance they could have been mistaken for human, if not for several differences that made them look increasingly alien the closer he got. From head to waist the attacker looked largely similar to Shepard himself, though perhaps not as heavily built. The most striking biological difference between them came when his gaze moved to their legs.

A human's legs were much straighter than those of the being before him, whose shins curved backwards, leading down to feet with far fewer toes than his own species possessed. A more than cursory look at their upper body would have likewise revealed the situation was the same regarding their hands, which only had two fingers and thumb each. By far the most identifiable overall feature, however, was the enviro-suit the figure wore, which was coloured a dull yellow, with a full-face visor of a brighter shade of the same colour covering their features almost completely, only the tip of their nose visible.

As well as the pair of white eyes that stared back at him.

His stomach heaved. Shepard turned away from the dead quarian, but it was too late. He braced his hands on his knees as he vomited, his body purging itself of its last meal as though it were trying to expel itself of the foulest poison imaginable. Trembling all over, he wiped his mouth with the back of his arm, returning his gaze to the corpse, which much like the marine's was surrounded by an expanding pool of red blood.

_It's not her. It's not her. It's not her._

It was at that moment he realised he had never killed a quarian before. In all the years that had passed since first joining the Alliance military, Shepard had fought and killed so many he had lost count. Humans, turians, asari, salarians, krogan, batarians, vorcha, it seemed that at least once he had found himself staring down the sights of a gun at a member of every species in the galaxy.

But never had he killed a quarian.

The cold and logical part of him noted it hadn't been difficult. The man he had killed had died as easily as a human or asari would have, the tiny fragment of metal the same size as the grains of sand around him having smashed the fragile organ in the quarian's chest to a pulp so quickly he hadn't even had time to worry about dying of infection. Shepard had never enjoyed killing, but he had long ago accepted the possibility, however remote, that he could end up having to kill almost anybody in the galaxy. No, the mere fact he had killed a quarian in and of itself hadn't been what bothered him.

It had been the eyes. They were a different shade of white, darker than the pair that were so familiar, tinted yellow as well by the visor that covered them. They had been close enough, though. Close enough to remind him of Hackett's words when he had told Shepard the news, when he had screamed and thrashed against the restraints a small army of medical staff had tried to hold him with when he had refused to calm down.

* * *

"It's true, Commander," the admiral said firmly, never breaking eye-contact. "You of all people deserve the truth after everything you've done, so believe me when I say the quarians broke off all communications with humanity a week ago and have begun attacking us on sight."

"But that doesn't make any sense!" Shepard roared, nearly managing to throw off the multitude of men and women that were trying to hold him down as he shook his head wildly in denial. "Why would they do that?"

"Because they blame us for the losses they suffered against the Reapers!" Hackett shouted back, clearly realising he needed to get through and soon. "They lost two of their liveships during the space battle over Earth, and the turians don't have any food to spare after so many of their worlds were hit."

The older man seemed to deflate slightly as he noticed Shepard was beginning to slow, though he still fought against the hands trying to prevent him from hurting himself. "We don't know if the attacks are the result of individuals acting alone or direct orders from the Admiralty Board," he continued. "We have unconfirmed reports of a lone quarian in a colony in the Terminus Systems we were forced to evacuate for fear of Reaper attack. If the report is accurate, we're going to capture them and find out the truth. Until we know for sure, we have to proceed as though an official declaration of war has been issued."

Shepard allowed the last of his resistance to give out as the doctors and nurses around him finally succeeded in wrestling him to the bed. "Then I'm going on the mission," he stated firmly, eyes never wavering even as he was injected with a sedative. The last thing he saw was Hackett's grim expression as darkness overtook his vision.

* * *

He hadn't backed down from that stance upon awakening, keeping the pressure on until the admiral allowed him to go. Shepard trusted Hackett. He would have believed almost anything the other man could have told him. He had needed to see this for himself, though, and he had.

He barely noticed when Andrews and his squad returned and didn't respond to the other man's questions about what had happened. He simply allowed himself to be led back into the shuttle, Ladon soon vanishing behind them.

He was a human, and Tali was a quarian.

And their people might very well soon be at war with each other.


End file.
